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Update viewer to use prior studies for Hanging Protocols initialization and using those studies in HP Match Image process (added getStudyPriors and getStudyPriorsMap)

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This commit is contained in:
Emanuel F. Oliveira 2017-02-10 12:54:22 -02:00 committed by Eloízio Salgado
parent b9a3cf9da3
commit 4df18233c4
10 changed files with 335 additions and 155 deletions
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7
OHIFViewer/client/components/viewer/viewer.js
View File

@ -28,8 +28,11 @@ const initHangingProtocol = () => {
// Instantiate StudyMetadataSource: necessary for Hanging Protocol to get study metadata
const studyMetadataSource = new StudyList.classes.OHIFStudyMetadataSource();
// Get prior studies map
const studyPriorsMap = StudyList.functions.getStudyPriorsMap(studyMetadataList);
// Creates Protocol Engine object with required arguments
const ProtocolEngine = new HP.ProtocolEngine(layoutManager, studyMetadataList, [], studyMetadataSource);
const ProtocolEngine = new HP.ProtocolEngine(layoutManager, studyMetadataList, studyPriorsMap, studyMetadataSource);
// Sets up Hanging Protocol engine
HP.setEngine(ProtocolEngine);
@ -132,7 +135,7 @@ Template.viewer.onRendered(function() {
// To avoid first run
if (isOHIFViewerMainRendered) {
// To run only when ViewerMainRendered dependency has changed.
// To run only when OHIFViewerMainRendered dependency has changed.
// because initHangingProtocol can have other reactive components
Tracker.nonreactive(initHangingProtocol);
}

148
Packages/ohif-hanging-protocols/client/protocolEngine.js
View File

@ -4,6 +4,13 @@ import { _ } from 'meteor/underscore';
import { OHIF } from 'meteor/ohif:core';
import 'meteor/ohif:viewerbase';
/**
* Import Constants
*/
const StudyMetadata = OHIF.viewerbase.metadata.StudyMetadata;
const StudySummary = OHIF.viewerbase.metadata.StudySummary;
// Define a global variable that will be used to refer to the Protocol Engine
// It must be populated by HP.setEngine when the Viewer is initialized and a ProtocolEngine
// is instantiated on top of the LayoutManager. If the global ProtocolEngine variable remains
@ -171,18 +178,30 @@ HP.ProtocolEngine = class ProtocolEngine {
* @param {Array} relatedStudies Array of related studies
* @param {Object} studyMedadataSource Instance of StudyMetadataSource (ohif-viewerbase) Object to get study metadata
*/
constructor(LayoutManager, studies, relatedStudies, studyMetadataSource) {
OHIF.log.info('ProtocolEngine::constructor');
constructor(layoutManager, studies, priorStudies, studyMetadataSource) {
// -----------
// Validations
if (!(layoutManager instanceof OHIF.viewerbase.LayoutManager)) {
throw new OHIF.viewerbase.OHIFError('ProtocolEngine::constructor layoutManager is not an instance of LayoutManager');
}
if (!(studyMetadataSource instanceof OHIF.viewerbase.StudyMetadataSource)) {
throw new OHIF.viewerbase.OHIFError('ProtocolEngine::constructor studyMetadataSource is not an instance of StudyMetadataSource');
}
this.LayoutManager = LayoutManager;
// @TODO: Validate "studies" parameter
// --------------
// Initialization
this.LayoutManager = layoutManager;
this.studies = studies;
this.relatedStudies = relatedStudies;
this.priorStudies = priorStudies instanceof Map ? priorStudies : new Map();
this.studyMetadataSource = studyMetadataSource;
// Put protocol engine in a known states
this.reset();
// Create an array for new stage ids to be stored
@ -221,7 +240,7 @@ HP.ProtocolEngine = class ProtocolEngine {
return;
}
study.numberOfPriorsReferenced = this.getNumberOfAvailablePriors(study);
study.numberOfPriorsReferenced = this.getNumberOfAvailablePriors(study.getStudyInstanceUID());
const rule = new HP.ProtocolMatchingRule('numberOfPriorsReferenced', {
numericality: {
greaterThanOrEqualTo: protocol.numberOfPriorsReferenced
@ -312,69 +331,25 @@ HP.ProtocolEngine = class ProtocolEngine {
}
/**
* Calculates the number of previous studies in the cached StudyList that
* have the same patientId and an earlier study date
* Get the number of prior studies supplied in the priorStudies map property.
*
* @param study The input study
* @returns {any|*} The number of available prior studies with the same patientId
* @param {String} studyInstanceUID The StudyInstanceUID of the study whose priors are needed
* @returns {number} The number of available prior studies with the same PatientID
*/
getNumberOfAvailablePriors(study) {
const instance = study.getFirstInstance();
const studies = StudyListStudies.find({
patientId: instance.getRawValue('x00100020'), // PatientID,
studyDate: {
$lt: instance.getRawValue('x00080020') // StudyDate
}
});
return studies.count();
getNumberOfAvailablePriors(studyInstanceUID) {
const priors = this.getAvailableStudyPriors(studyInstanceUID);
return priors.length;
}
findRelatedStudies(protocol, study) {
if (!protocol.protocolMatchingRules) {
return;
}
var studies = StudyListStudies.find({
patientId: study.patientId,
studyDate: {
$lt: study.studyDate
}
}, {
sort: {
studyDate: -1
}
});
var related = [];
var currentDate = moment(study.studyDate, 'YYYYMMDD');
studies.forEach(function(priorStudy, priorIndex) {
// Calculate an abstract prior value for the study in question
if (priorIndex === (studies.length - 1)) {
priorStudy.abstractPriorValue = -1;
} else {
// Abstract prior index starts from 1 in the DICOM standard
priorStudy.abstractPriorValue = priorIndex + 1;
}
// Calculate the relative time using Moment.js
var priorDate = moment(priorStudy.studyDate, 'YYYYMMDD');
priorStudy.relativeTime = currentDate.diff(priorDate);
var details = HP.match(priorStudy, protocol.protocolMatchingRules);
if (details.score) {
related.push({
score: details.score,
study: priorStudy
});
}
});
sortByScore(related);
return related.map(function(v) {
return v.study;
});
/**
* Get the array prior studies from a specific study.
*
* @param {String} studyInstanceUID The StudyInstanceUID of the study whose priors are needed
* @returns {Array} The array of available priors or an empty array
*/
getAvailableStudyPriors(studyInstanceUID) {
const priors = this.priorStudies.get(studyInstanceUID);
return priors instanceof Array ? priors : [];
}
// Match images given a list of Studies and a Viewport's image matching reqs
@ -403,17 +378,7 @@ HP.ProtocolEngine = class ProtocolEngine {
abstractPriorValue = parseInt(abstractPriorValue, 10);
// TODO: Restrict or clarify validators for abstractPriorValue?
// @TODO replace for this.relatedStudies (TypeSafeCollection of StudyMetadatas)
const studies = StudyListStudies.find({
patientId: currentStudy.patientId,
studyDate: {
$lt: currentStudy.studyDate
}
}, {
sort: {
studyDate: -1
}
}).fetch();
const studies = this.getAvailableStudyPriors(currentStudy.getStudyInstanceUID());
// TODO: Revisit this later: What about two studies with the same
// study date?
@ -426,25 +391,40 @@ HP.ProtocolEngine = class ProtocolEngine {
priorStudy = studies[studyIndex];
}
if (!priorStudy) {
if (!(priorStudy instanceof StudyMetadata) && !(priorStudy instanceof StudySummary)) {
return;
}
// @TODO: Make sure this study is already loaded into the viewer (OHIF.viewer.Studies)
// @TypeSafeStudies
const priorStudyInstanceUID = priorStudy.getStudyInstanceUID();
const alreadyLoaded = OHIF.viewer.Studies.findBy({
studyInstanceUid: priorStudy.studyInstanceUid
studyInstanceUid: priorStudyInstanceUID
});
if (!alreadyLoaded) {
this.studyMetadataSource.getByInstanceUID(priorStudy.studyInstanceUid, study => {
this.studyMetadataSource.getByInstanceUID(priorStudyInstanceUID).then(study => {
study.abstractPriorValue = abstractPriorValue;
study.displaySets = OHIF.viewerbase.sortingManager.getDisplaySets(study);
OHIF.viewer.Studies.insert(study);
this.studies.push(study);
this.matchImages(viewport);
this.updateViewports();
});
const studyMetadata = new OHIF.metadata.StudyMetadata(study);
const displaySets = OHIF.viewerbase.sortingManager.getDisplaySets(studyMetadata);
studyMetadata.setDisplaySets(displaySets);
study.selected = true;
study.displaySets = displaySets;
OHIF.viewer.Studies.insert(study);
OHIF.viewer.StudyMetadataList.insert(studyMetadata);
}, error => { console.alert(error) });
// this.studyMetadataSource.getByInstanceUID(priorStudy.studyInstanceUid).then(, study => {
// study.abstractPriorValue = abstractPriorValue;
// study.displaySets = OHIF.viewerbase.sortingManager.getDisplaySets(study);
// OHIF.viewer.Studies.insert(study);
// this.studies.push(study);
// this.matchImages(viewport);
// this.updateViewports();
// });
}
}
// TODO: Add relative Date / time

12
Packages/ohif-study-list/client/lib/OHIFStudySummary.js Normal file
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@ -0,0 +1,12 @@
import { OHIF } from 'meteor/ohif:core';
import 'meteor/ohif:viewerbase';
export class OHIFStudySummary extends OHIF.viewerbase.metadata.StudySummary {
// @Override
addTags(tagMap) {
// @TODO: Map OHIF tag names to standard DICOM tag names
super.addTags(tagMap);
}
}

52
Packages/ohif-study-list/client/lib/getStudyPriors.js Normal file
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@ -0,0 +1,52 @@
import { OHIF } from 'meteor/ohif:core';
import 'meteor/ohif:viewerbase';
// Local Dependencies
import { OHIFStudySummary } from './OHIFStudySummary';
const StudyMetadata = OHIF.viewerbase.metadata.StudyMetadata;
const StudySummary = OHIF.viewerbase.metadata.StudySummary;
const PatientID = 'x00100020';
const StudyDate = 'x00080020';
const getStudyPriors = study => {
const priorStudies = [];
let patientID;
let studyDate;
if (study instanceof StudyMetadata) {
const instance = study.getFirstInstance();
patientID = instance.getRawValue(PatientID); // PatientID
studyDate = instance.getRawValue(StudyDate); // StudyDate
} else if (study instanceof StudySummary) {
patientID = study.getTagValue(PatientID); // PatientID
studyDate = study.getTagValue(StudyDate); // StudyDate
}
// Find prior studies in global StudyListStudies Minimongo collection...
const cursor = StudyListStudies.find({
patientId: patientID,
studyDate: {
$lt: studyDate
}
}, {
sort: {
studyDate: 'desc'
}
});
// Create an OHIFStudySummary object for each prior study found...
cursor.forEach(study => {
const summary = new OHIFStudySummary();
summary.addTags(study);
priorStudies.push(summary);
console.log('@StudyListStudies');
console.log(study);
console.log(study);
});
return priorStudies;
};
export { getStudyPriors };

33
Packages/ohif-study-list/client/lib/getStudyPriorsMap.js Normal file
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@ -0,0 +1,33 @@
import { OHIF } from 'meteor/ohif:core';
import 'meteor/ohif:viewerbase';
// Local Dependencies
import { getStudyPriors } from './getStudyPriors';
const StudyMetadata = OHIF.viewerbase.metadata.StudyMetadata;
const StudySummary = OHIF.viewerbase.metadata.StudySummary;
/**
* Create a Map of study priors where the key of each entry is the StudyInstanceUID and its value is an array of StudySummary instances.
* @returns {Map} The study map.
*/
const getStudyPriorsMap = studies => {
const priorsMap = new Map();
if (studies instanceof Array) {
studies.forEach(study => {
if (study instanceof StudyMetadata || study instanceof StudySummary) {
const studyInstanceUID = study.getStudyInstanceUID();
if (studyInstanceUID) {
const priors = getStudyPriors(study);
priorsMap.set(studyInstanceUID, priors);
}
}
});
}
return priorsMap;
};
export { getStudyPriorsMap };

13
Packages/ohif-study-list/client/lib/studylist.js
View File

@ -1,11 +1,20 @@
import { Viewerbase } from 'meteor/ohif:viewerbase';
// Classes
import { OHIFStudyMetadataSource } from './OHIFStudyMetadataSource';
import { OHIFStudySummary } from './OHIFStudySummary';
// Functions
import { getStudyPriors } from './getStudyPriors';
import { getStudyPriorsMap } from './getStudyPriorsMap';
StudyList = {
functions: {},
functions: {
getStudyPriors,
getStudyPriorsMap
},
callbacks: {},
classes: {
OHIFStudyMetadataSource
OHIFStudyMetadataSource,
OHIFStudySummary
}
};

3
Packages/ohif-viewerbase/client/index.js
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@ -188,7 +188,8 @@ Viewerbase.ResizeViewportManager = ResizeViewportManager;
import { StudyMetadata } from './lib/classes/metadata/StudyMetadata';
import { SeriesMetadata } from './lib/classes/metadata/SeriesMetadata';
import { InstanceMetadata } from './lib/classes/metadata/InstanceMetadata';
Viewerbase.metadata = { StudyMetadata, SeriesMetadata, InstanceMetadata };
import { StudySummary } from './lib/classes/metadata/StudySummary';
Viewerbase.metadata = { StudyMetadata, SeriesMetadata, InstanceMetadata, StudySummary };
// TypeSafeCollection
import { TypeSafeCollection } from './lib/classes/TypeSafeCollection';

119
Packages/ohif-viewerbase/client/lib/DICOMTagDescriptions.js
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@ -1,6 +1,7 @@
const NUMBER = 'number';
const STRING = 'string';
const REGEX_TAG = /^x[0-9a-fx]{8}$/;
const DICOMTagDescriptions = Object.create(Object.prototype, {
_descriptions: {
@ -9,22 +10,94 @@ const DICOMTagDescriptions = Object.create(Object.prototype, {
writable: false,
value: Object.create(null)
},
tagNumberToString: {
configurable: false,
enumerable: true,
writable: false,
value: function tagNumberToString(tag) {
let string; // by default, undefined is returned...
if (this.isValidTagNumber(tag)) {
// if it's a number, build its hexadecimal representation...
string = 'x' + ('00000000' + tag.toString(16)).substr(-8);
}
return string;
}
},
isValidTagNumber: {
configurable: false,
enumerable: true,
writable: false,
value: function isValidTagNumber(tag) {
return (typeof tag === NUMBER && tag >= 0 && tag <= 0xFFFFFFFF);
}
},
isValidTag: {
configurable: false,
enumerable: true,
writable: false,
value: function isValidTag(tag) {
return (typeof tag === STRING ? REGEX_TAG.test(tag) : this.isValidTagNumber(tag));
}
},
find: {
configurable: false,
enumerable: true,
writable: false,
value: function find(name) {
let description; // by default, undefined...
if (typeof name === NUMBER) {
// if it's a number, build its hexadecimal representation...
name = 'x' + ('00000000' + name.toString(16)).substr(-8);
let description; // by default, undefined is returned...
if (typeof name !== STRING) {
// if it's a number, a tag string will be returned...
name = this.tagNumberToString(name);
}
if (typeof name === STRING) {
description = this._descriptions[name];
}
return description;
}
}
},
init: {
configurable: false,
enumerable: true,
writable: false,
value: function init(descriptionMap) {
const _hasOwn = Object.prototype.hasOwnProperty;
const _descriptions = this._descriptions;
for (let tag in descriptionMap) {
if (_hasOwn.call(descriptionMap, tag)) {
if (!this.isValidTag(tag)) {
// Skip in case tag is not valid...
console.info(`DICOMTagDescriptions: Invalid tag "${tag}"...`);
continue;
}
if (tag in _descriptions) {
// Skip in case the tag is duplicated...
console.info(`DICOMTagDescriptions: Duplicated tag "${tag}"...`);
continue;
}
// Save keyword...
const keyword = descriptionMap[tag];
// Create a description entry and freeze it...
const entry = Object.create(null);
entry.tag = tag;
entry.keyword = keyword;
Object.freeze(entry);
// Add tag references to entry...
_descriptions[tag] = entry;
// Add keyword references to entry (if not present already)...
if (keyword in _descriptions) {
const currentEntry = _descriptions[keyword];
console.info(`DICOMTagDescriptions: Using <${currentEntry.tag},${currentEntry.keyword}> instead of <${entry.tag},${entry.keyword}> for keyword "${keyword}"...`);
} else {
_descriptions[keyword] = entry;
}
}
}
// Freeze internal description map...
Object.freeze(_descriptions);
// Freeze itself...
Object.freeze(this);
}
},
});
/**
@ -3179,41 +3252,7 @@ let initialTagDescriptionMap = {
xfffee0dd: 'EndOfSequence'
};
// Safely populate DICOMTagDescriptions object
(function(initialTagDescriptionMap) {
const _hasOwn = Object.prototype.hasOwnProperty;
const descriptionMap = DICOMTagDescriptions._descriptions;
for (let tag in initialTagDescriptionMap) {
if (_hasOwn.call(initialTagDescriptionMap, tag)) {
if (tag in descriptionMap) {
// Skip in case the tag is duplicated...
console.info(`DICOMTagDescriptions: Duplicated tag ${tag}...`);
continue;
}
// Save keyword...
const keyword = initialTagDescriptionMap[tag];
// Create a description entry and freeze it...
const entry = Object.create(null);
entry.tag = tag;
entry.keyword = keyword;
Object.freeze(entry);
// Add tag references to entry...
descriptionMap[tag] = entry;
// Add keyword references to entry (if not present already)...
if (keyword in descriptionMap) {
const currentEntry = descriptionMap[keyword];
console.info(`DICOMTagDescriptions: Using <${currentEntry.tag},${currentEntry.keyword}> instead of <${entry.tag},${entry.keyword}> for keyword "${keyword}"...`);
} else {
descriptionMap[keyword] = entry;
}
}
}
// Freeze internal description map (nothing should be changed in this object afterwords)...
Object.freeze(descriptionMap);
}(initialTagDescriptionMap));
// Freeze exported object...
Object.freeze(DICOMTagDescriptions);
DICOMTagDescriptions.init(initialTagDescriptionMap);
// Discard original map...
initialTagDescriptionMap = null;

1
Packages/ohif-viewerbase/client/lib/classes/metadata/InstanceMetadata.js
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@ -4,7 +4,6 @@ import { OHIFError } from '../OHIFError';
const UNDEFINED = 'undefined';
const NUMBER = 'number';
const STRING = 'string';
const REGEX_TAG = /^x[0-9a-fx]{8}$/;
export class InstanceMetadata extends Metadata {

102
Packages/ohif-viewerbase/client/lib/classes/metadata/StudySummary.js
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@ -1,42 +1,94 @@
import { DICOMTagDescriptions } from '../../DICOMTagDescriptions';
class StudySummary {
const StudyInstanceUID = 'x0020000D';
constructor(propertyMap) {
export class StudySummary {
constructor(tagMap, propertyMap) {
// Define the main immutable "_data" private property.
Object.defineProperty(this, '_data', {
configurable: false,
enumerable: false,
writable: false,
value: Object.create(null)
Object.defineProperties(this, {
_tags: {
configurable: false,
enumerable: false,
writable: false,
value: Object.create(null)
},
_properties: {
configurable: false,
enumerable: false,
writable: false,
value: Object.create(null)
}
});
const hasOwn = Object.prototype.hasOwnProperty;
const data = this._data;
for (let property in propertyMap) {
if (hasOwn.call(propertyMap, property)) {
data[property] = propertyMap[property];
}
// Initialize internal tag map if first argument is given.
if (tagMap !== void 0) {
this.addTags(tagMap);
}
// Initialize internal property map if second argument is given.
if (propertyMap !== void 0) {
this.addProperties(addProperties);
}
}
getStudyInstanceUID() {
// This method should return null if StudyInstanceUID is not available to keep compatibility StudyMetadata API
return this.getTagValue(StudyInstanceUID) || null;
}
addProperties(propertyMap) {
const _hasOwn = Object.prototype.hasOwnProperty;
const _properties = this._properties;
for (let property in propertyMap) {
if (_hasOwn.call(propertyMap, property)) {
_properties[property] = propertyMap[property];
}
}
}
addTags(tagMap) {
const _hasOwn = Object.prototype.hasOwnProperty;
const _tags = this._tags;
for (let tag in tagMap) {
if (_hasOwn.call(tagMap, tag)) {
const description = DICOMTagDescriptions.find(tag);
// When a description is available, use its tag as internal key...
if (description) {
_tags[description.tag] = tagMap[tag];
} else {
_tags[tag] = tagMap[tag];
}
}
}
}
tagExists(tagName) {
const _tags = this._tags;
const description = DICOMTagDescriptions.find(tagName);
if (description) {
return (description.tag in _tags);
}
return (tagName in _tags);
}
getTagValue(tagName) {
const _tags = this._tags;
const description = DICOMTagDescriptions.find(tagName);
if (description) {
return _tags[description.tag];
}
return _tags[tagName];
}
propertyExists(propertyName) {
const internalPropertyName = this.getInternalPropertyName(propertyName);
return (internalPropertyName in this._data);
return (propertyName in this._properties);
}
getPropertyValue(propertyName) {
const internalPropertyName = this.getInternalPropertyName(propertyName);
return this._data[internalPropertyName];
}
/**
* This function is supposed to translate external property names into internal property names.
* By default it implements the simplest translation possible.
*/
getInternalPropertyName(propertyName) {
return propertyName;
return this._properties[propertyName];
}
}